How to paint alpha emissive mask ?
First of all, you are going to want to UV unwrap your cube by going into edit mode and using something like "Smart UV Project." If you then go into the "UV / Image Editor" panel, you should see your faces outlined. Go ahead and hit the new button next to the +, and leave the color as black. Click OK and select paint mode from the drop down bar next to the button with a picture of a pin on it. You can now drag while clicking to paint over your texture. When you are done, select "Image > Save as Image" and name and save your texture. If you don't, the texture will be gone when you reopen the blend file. Your texture should look something like this:


Now, go back into your "Node Editor" panel, and add a new emission shader, mix shader, and Image Texture. Connect the your base, non-glowing material to the top "shader" input of the mix shader, the emission shader to the bottom "shader" input, and your Image Texture "Color" to the "Fac" input. Finally, in the Image Texture node, select the texture you drew on earlier. What this does is, in the white areas of your texture, the emission is able to show through, whereas the black areas let the base shader show through. Here's a picture of how it should all have come together:


In the end, your result should look something like this: 

Have fun Blendering! Cheers, 
Graves Broderick